Background: Human respiratory syncytial virus (HRSV) is a major cause of
severe viral acute respiratory illness and contributes significantly to
severe pneumonia cases in Africa. Little is known about its
spatial-temporal distribution as defined by its genetic diversity.
Methods: A retrospective study conducted utilizing archived
nasopharyngeal specimens from patients attending outpatient clinics in
hospitals located in five demographically and climatically distinct
regions of Kenya; Coast, Western, Highlands, Eastern and Nairobi. The
viral total RNA was extracted and tested using multiplex real time
RT-PCR (reverse transcriptase polymerase chain reaction). A segment of
the G-gene was amplified using one-step RT-PCR and sequenced by Sanger
di-deoxy method. Bayesian analysis of phylogeny was utilized and
subsequently median joining methods for haplotype network
reconstruction. Results: Three genotypes of HRSVA were detected; GA5
(14.0%), GA2 (33.1%) and NA1 (52.9%). HRSVA prevalence varied by
location from 33% to 13.2% in the Highlands and the Eastern regions
respectively. The mean nucleotide diversity (Pi(π)) varied by genotype:
highest of 0.018 for GA5 and lowest of 0.005 for NA1. A total of 58
haplotypes were identified (GA5 10; GA2 20; NA1 28). These haplotypes
were introduced into the population locally by single haplotypes and
additional subsidiary seeds amongst the GA2 and the NA1 haplotypes.
Conclusions: HRSVA was found across all the regions throughout the study
period and comprised three genotypes; GA5, GA2 and NA1 genotypes. The
genotypes were disproportionately distributed across the regions with
GA5 gradually increasing towards the Western zones and decreasing
towards the Eastern zones of the country.
Semiquantitative one-step RT-PCR for simultaneous identification of human influenza and respiratory syncytial viruses
